New variants arising from mutations within the SARS-CoV-2 genome could subsequently lead to increased mortality and morbidity in COVID-19 patients. Microbiota within the human respiratory tract is part of the immune system that can provide protection from infection, including from SARS-CoV-2. Unfortunately, the pathogenesis of various SARS-CoV-2 variants can interfere with the homeostasis of microbial community in the respiratory tract. It is therefore imperative to study the bacterial community profile within the respiratory tract of COVID-19 patients having different SARS-CoV-2 variants. In this study, we identified SARS-CoV-2 variants using whole genome sequencing of naso/oropharyngeal swabs of confirmed COVID-19 patients with Oxford Nanopore Technologies (ONT), followed by 16S rRNA gene amplicon sequencing to assess the bacterial community diversity. Sequencing of 23 selected isolates …